-
Article
Selami Baglamis, Vivek M. Sheraton, Debora Meijer, Haibin Qian, Ron A. Hoebe, Kristiaan J. Lenos, Max A. Betjes, Sander Tans, Jeroen van Zon, Louis Vermeulen, and Przemek M. Krawczyk.
Using picoliter droplet deposition to track clonal competition in adherent and organoid cancer cell cultures.
Scientific Reports
13, 18832.
-
Article
L. Crielaard, R. Quax, A. D. M. Sawyer, V. V. Vasconcelos, M. Nicolaou, K. Stronks, and P. M. A. Sloot.
Using network analysis to identify leverage points based on causal loop diagrams leads to false inference.
Scientific Reports
13(1), 21046.
-
Article
A. Ralli, T. Weaving, A. Tranter, W. M. Kirby, P. J. Love, and P. V. Coveney.
Unitary partitioning and the contextual subspace variational quantum eigensolver.
Physical Review Research
5(1), 013095.
-
Proceedings
Roland V. Bumbuc, H. Ibrahim Korkmaz, P. P. M. Van Zuijlen, Louis Vermeulen, and Vivek M. Sheraton.
Understanding the Dynamics of the Proliferative Phase in Local Burn Wound Healing.
In: Proceedings - 2023 2023 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2023.
ISBN 9798350337488.
pp. 3676-3683.
-
Article
C. Hourican, G. Peeters, R. J. F. Melis, S. L. Wezeman, T. M. Gill, M. G. M. Olde Rikkert, and R. Quax.
Understanding multimorbidity requires sign-disease networks and higher-order interactions, a perspective.
Frontiers in Systems Biology
3, 1155599.
-
Proceedings
Marcel Geller, Vítor V. Vasconcelos, and Flávio L. Pinheiro.
Toxicity in Evolving Twitter Topics.
In:
Computational Science – ICCS 2023.
ISBN
9783031360268.
IV, pp. 40-54.
-
Article
M. T. Wortel, D. Agashe, S. F. Bailey, C. Bank, K. Bisschop, T. Blankers, J. Cairns, E. S. Colizzi, D. Cusseddu, M. M. Desai, B. van Dijk, M. Egas, J. Ellers, A. T. Groot, D. G. Heckel, M. L. Johnson, K. Kraaijeveld, J. Krug, L. Laan, M. Lässig, P. A. Lind, J. Meijer, L. M. Noble, S. Okasha, P. B. Rainey, D. E. Rozen, S. Shitut, S. J. Tans, O. Tenaillon, H. Teotónio, J. A. G. M. de Visser, M. E. Visser, R. M. A. Vroomans, G. D. A. Werner, B. Wertheim, and P. S. Pennings.
Towards evolutionary predictions: Current promises and challenges.
Evolutionary Applications
16(1), pp. 3-21.
-
Article
U. Chavez-Baldini, D. H. Nieman, A. Keestra, A. Lok, R. J. T. Mocking, P. de Koning, V. V. Krzhizhanovskaya, C. L. H. Bockting, G. van Rooijen, D. J. A. Smit, A. L. Sutterland, K. J. H. Verweij, G. van Wingen, J. T. W. Wigman, N. C. Vulink, and D. Denys.
The relationship between cognitive functioning and psychopathology in patients with psychiatric disorders.
Psychological Medicine
53(2), pp. 476-485.
-
Article
A. R. Tilman, V. V. Vasconcelos, E. Akçay, and J. B. Plotkin.
The evolution of forecasting for decision-making in dynamic environments.
Collective Intelligence
2(4).
-
Article
X. Zhou, A. Belloum, M. H. Lees, T. van Engers, and C. de Laat.
The dynamics of corruption under an optional external supervision service.
Applied Mathematics and Computation
457, 128172.
-
Article
-
Article
H. F. Willard, E. S. Deutekom, D. Allemand, S. Tambutté, and J. A. Kaandorp.
Testing hypotheses on the calcification in scleractinian corals using a spatio-temporal model that shows a high degree of robustness.
Journal of Theoretical Biology
561(21), 111382.
-
Article
M. K. Bieniek, A. D. Wade, A. P. Bhati, S. Wan, and P. V. Coveney.
TIES 2.0: A dual-topology open source relative binding free energy builder with web portal.
Journal of Chemical Information and Modeling
63(3), pp. 718-724.
-
Article
K. Ahmad, A. Javed, C. Lanphere, P. V. Coveney, E. V. Orlova, and S. Howorka.
Structure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations.
Nature Communications
14, 3630.
-
Article
J. F. Uleman, R. J. F. Melis, E. Ntanasi, N. Scarmeas, A. G. Hoekstra, R. Quax, and M. G. M. Olde Rikkert.
Simulating the multicausality of Alzheimer's disease with system dynamics.
Alzheimer's & Dementia
19(6), pp. 2633-2654.
-
Proceedings
C. J. Spieker, K. Asteriou, and G. Zav́odszky.
Simulating Initial Steps of Platelet Aggregate Formation in a Cellular Blood Flow Environment.
In: Computational Science – ICCS 2023.
ISBN 9783031360244.
III, pp. 323-336.
-
Article
A. W. van Beurden, J. M. Meylahn, S. Achterhof, R. Buijink, A. Olde Engberink, S. Michel, J. H. Meijer, and J. H. T. Rohling.
Reduced Plasticity in Coupling Strength in the Aging SCN Clock as Revealed by Kuramoto Modeling.
Journal of biological rhythms
38(5), pp. 461-475.
-
Article
K. van der Zwet, A. I. Barros, T. M. van Engers, and P. M. A. Sloot.
Promises and pitfalls of computational modelling for insurgency conflicts.
The Journal of Defense Modeling and Simulation: Applications, Methodology, Technology
20(3), pp. 333-350.
-
Proceedings
Y. Demchenko, V. Degeler, A. Opresu, and S. Brewer.
Professional and 21st Century Skills for Data Driven Digital Economy.
In: 2023 IEEE Global Engineering Education Conference (EDUCON).
ISBN 9798350399431.
pp. 847-854.
-
Proceedings
-
Proceedings
-
Article
-
Article
M. Klöwer, P. V. Coveney, E. A. Paxton, and T. N. Palmer.
Periodic orbits in chaotic systems simulated at low precision.
Scientific Reports
13, 11410.
-
Article
S. Wang, X. Chen, Z. Xiao, A. Szolnoki, and V. V. Vasconcelos.
Optimization of institutional incentives for cooperation in structured populations.
Journal of the Royal Society Interface
20(199), 20220653.
-
Article
B. Nottrot, E. Folmer, D. Roy, B. Scheer, and P. Merx.
Multi-unit building address geocoding: An approach without indoor location reference data.
Transactions in GIS
27(1), pp. 57-83.
-
Proceedings
Roland V. Bumbuc, Vehpi Yildirim, and M. Vivek Sheraton.
Modelling the Interplay Between Chronic Stress and Type 2 Diabetes On-Set.
In: Computational Science – ICCS 2023.
ISBN 9783031360206.
II, pp. 330-338.
-
Article
M. Boersma, J. Wolsink, S. Sourabh, L. A. Hoogduin, and D. Kandhai.
Measure cross-sectoral structural similarities from financial networks.
Scientific Reports
13, 7124.
-
Proceedings
C. Dupont and D. Roy.
Manifold Analysis for High-Dimensional Socio-Environmental Surveys.
In:
Computational Science – ICCS 2023.
ISBN
9783031360275.
IV, pp. 25-39.
-
Article
A. P. Bhati, A. Hoti, A. Potterton, M. K. Bieniek, and P. V. Coveney.
Long Time Scale Ensemble Methods in Molecular Dynamics: Ligand-Protein Interactions and Allostery in SARS-CoV-2 Targets.
Journal of Chemical Theory and Computation
19(11), pp. 3359-3378.
-
Article
Alex Gabel, Victoria Klein, Riccardo Valperga, Jeroen S. W. Lamb, Kevin Webster, Rick Quax, and Efstratios Gavves.
Learning Lie Group Symmetry Transformations with Neural Networks.
Proceedings of Machine Learning Research
221, pp. 50-59.
-
Article
J. L. Suter, M. Vassaux, and P. V. Coveney.
Large-scale molecular dynamics elucidates the mechanics of reinforcement in graphene-based composites.
Advanced materials
35(35), e2302237.
-
Article
S. Kakhaia, P. Zun, D. Ye, and V. Krzhizhanovskaya.
Inverse uncertainty quantification of a mechanical model of arterial tissue with surrogate modelling.
Reliability Engineering & System Safety
238, 109393.
-
Article
W. Barfuss and J. M. Meylahn.
Intrinsic fluctuations of reinforcement learning promote cooperation.
Scientific Reports
13, 1309.
-
Article
C. J. Spieker, G. Závodszky, C. Mouriaux, P. H. Mangin, and A. G. Hoekstra.
Initial platelet aggregation in the complex shear environment of a punctured vessel model.
Physics of Fluids
35(7), 071904.
-
Proceedings
A. Fuertes Blanco, Z. Shi, D. Roy, and Z. Zhao.
Improving the Resiliency of Decentralized Crowdsourced Blockchain Oracles.
In:
Computational Science – ICCS 2023.
ISBN
9783031359958.
I, pp. 3-17.
-
Article
K. Ly, Y. Kashnitsky, S. Chamezopoulos, and V. Krzhizhanovskaya.
Improving Article Classification with Edge-Heterogeneous Graph Neural Networks.
-
Article
Y. Hao, G. Závodszky, C. Tersteeg, M. Barzegari, and A. G. Hoekstra.
Image-based flow simulation of platelet aggregates under different shear rates.
PLoS Computational Biology
19(7), e1010965.
-
Article
Haibin Qian, Selami Baglamis, Fumei Redeker, Julia Raaijman, Ron A. Hoebe, Vivek M. Sheraton, Louis Vermeulen, and Przemek M. Krawczyk.
High-Content and High-Throughput Clonogenic Survival Assay Using Fluorescence Barcoding.
Cancers
15(19), 4772.
-
Article
J. W. S. McCullough and P. V. Coveney.
High resolution simulation of basilar artery infarct and flow within the circle of Willis.
Scientific Reports
13, 21665.
-
Proceedings
V. Bazyleva, V. M. Garibay, and D. Roy.
Global Sensitivity Analysis Using Polynomial Chaos Expansion on the Grassmann Manifold.
In:
Computational Science – ICCS 2023.
ISBN
9783031360305.
V, pp. 583-597.
-
Article
D. Groen, H. Arabnejad, D. Suleimenova, W. Edeling, Erwan Raffin, Y. Xue, K. Bronik, N. Monnier, and P. V. Coveney.
FabSim3: An automation toolkit for verified simulations using high performance computing.
Computer Physics Communications
283, 108596.
-
Article
J. F. Uleman, R. J. F. Melis, A. G. Hoekstra, M. G. M. Olde Rikkert, and R. Quax.
Exploring the potential impact of multi-factor precision interventions in Alzheimer's disease with system dynamics.
Journal of Biomedical Informatics
145, 104462.
-
Article
S. Wan, A. P. Bhati, A. D. Wade, and P. V. Coveney.
Ensemble-Based Approaches Ensure Reliability and Reproducibility.
Journal of Chemical Information and Modeling
63(22), pp. 6959-6963.
-
Proceedings
M. H. N. Yousefi, V. Degeler, and A. Lazovik.
Empowering Machine Learning Development with Service-Oriented Computing Principles.
In: Service-Oriented Computing - 17th Symposium and Summer School, SummerSOC 2023, Revised Selected Papers.
ISBN 9783031457289.
pp. 24-44.
-
Article
A. R. Schuurman, P. M. A. Sloot, W. J. Wiersinga, and T. van der Poll.
Embracing complexity in sepsis.
Critical Care
27, 102.
-
Article
I. Zacharoudiou, J. W. S. McCullough, and P. V. Coveney.
Development and performance of a HemeLB GPU code for human-scale blood flow simulation.
Computer Physics Communications
282(108548), 108548.
-
Proceedings
J. Nevin, P. Groth, and M. Lees.
Data Integration Landscapes.
In:
Computational Science – ICCS 2023.
ISBN
9783031359958.
I, pp. 494-508.
-
Article
J. R. Helmus and R. Wolbertus.
Cooperative behaviour at public electric vehicle charging stations.
Travel Behaviour and Society
32, 100572.
-
PhD Thesis
K. van der Zwet.
Computational models of emergent organisation in conflict environments.
ISBN
9789464731811.
Supervised by
P. M. A. Sloot, T. M. van Engers, and A. I. Barros.
-
Article
S. Wan, A. P. Bhati, and P. V. Coveney.
Comparison of Equilibrium and Nonequilibrium Approaches for Relative Binding Free Energy Predictions.
Journal of Chemical Theory and Computation
19(21), pp. 7846-7860.
-
Proceedings
J. Kwak, M. H. Lees, and W. Cai.
Characterization of Pedestrian Contact Interaction Trajectories.
In:
Computational Science – ICCS 2023.
ISBN
9783031359958.
I, pp. 18-32.
-
Article
A. Mutlu, D. Roy, and T. Filatova.
Capitalized value of evolving flood risks discount and nature-based solution premiums on property prices.
Ecological Economics
205, 107682.
-
Proceedings
J. van Dijk, G. Zavodszky, A.-L. Varbanescu, A. D. Pimentel, and A. Hoekstra.
Building a Fine-Grained Analytical Performance Model for Complex Scientific Simulations.
In:
Parallel Processing and Applied Mathematics.
ISBN
9783031304422.
I, pp. 183-196.
-
Article
R. A. Manzuk, A. C. Maloof, J. A. Kaandorp, and M. Webster.
Branching archaeocyaths as ecosystem engineers during the Cambrian radiation.
Geobiology
21(1), pp. 66-85.
-
Article
T. Weaving, A. Ralli, W. M. Kirby, P. J. Love, S. Succi, and P. V. Coveney.
Benchmarking noisy intermediate scale quantum error mitigation strategies for ground state preparation of the HCl molecule.
Physical Review Research
5(4), 043054.
-
Article
Rémy Petkantchin, Alexandre Rousseau, Omer Eker, Karim Zouaoui Boudjeltia, Franck Raynaud, Bastien Chopard, Alfons Hoekstra, Raymond Padmos, Victor Azizi, Claire Miller, and Max van der Kolk.
Author Correction: A simplified mesoscale 3D model for characterizing fibrinolysis under flow conditions.
Scientific Reports
13, 20369.
-
Article
L. Wang, A. C. Pronk, E. P. van Poelgeest, R. Briggs, J. A. H. R. Claassen, S. Jansen, M. Klop, F. J. de Lange, C. C. G. M. Meskers, V. J. J. Odekerken, S. J. Payne, M. C. Trappenburg, R. D. Thijs, J. F. Uleman, A. G. Hoekstra, and N. van der Velde.
Applying systems thinking to unravel the mechanisms underlying orthostatic hypotension related fall risk.
GeroScience
45(4), pp. 2743-2755.
-
Article
J. Nevin, P. Groth, and M. Lees.
An approach for analysing the impact of data integration on complex network diffusion models.
Journal of complex networks
11(4), cnad025.
-
Article
T. Weaving, A. Ralli, W. M. Kirby, A. Tranter, P. J. Love, and P. V. Coveney.
A stabilizer framework for the Contextual Subspace Variational Quantum Eigensolver and the noncontextual projection ansatz.
Journal of Chemical Theory and Computation
19(3), pp. 808-821.
-
Article
R. Petkantchin, A. Rousseau, O. Eker, K. Zouaoui Boudjeltia, F. Raynaud, B. Chopard, A. Hoekstra, R. Padmos, V. Azizi, C. Miller, and M. van der Kolk.
A simplified mesoscale 3D model for characterizing fibrinolysis under flow conditions.
Scientific Reports
13, 13681.
-
Article
A. O. Rydin, Y. Milaneschi, R. Quax, J. Li, J. A. Bosch, R. A. Schoevers, E. J. Giltay, B. W. J. H. Penninx, and F. Lamers.
A network analysis of depressive symptoms and metabolomics.
Psychological Medicine
53(15), pp. 7385-7394.
-
Article
V. Yildirim, V. M. Sheraton, R. Brands, L. Crielaard, R. Quax, N. A. W. van Riel, K. Stronks, M. Nicolaou, and P. M. A. Sloot.
A data-driven computational model for obesity-driven diabetes onset and remission through weight loss.
iScience
26(11), 108324.
-
Proceedings
Angela Koloi, Vasileios S. Loukas, Antonis Sakellarios, Jos A. Bosch, Rick Quax, Karina Nowakowska, Nikolaos Tachos, Jakub Kaźmierski, Costas Papaloukas, and Dimitrios Fotiadis.
A comparison study on creating simulated patient data for individuals suffering from chronic coronary disorders.
In:
2023 45th Annual International Conference of the IEEE Engineering in Medicine and Biology Conference, EMBC 2023 - Proceedings.
ISBN
9798350324471.
Publications of the CSL group